Virtual ChIP-seq Predictions for TF Binding in Cistrome and ENCODE-DREAM Datasets

Two gzipped tarballs contain BED files of Virtual ChIP-seq posterior probabilities for transcription factor binding. The data corresponds to predictions on specific chromosomes (chr5, chr10, chr15, chr20 for Cistrome; chr1, chr8, chr21 for ENCODE-DREAM) in validation cell types. The dataset was created by Mehran Karimzadeh of the University of Toronto.

Use Cases

• Benchmarking computational models for transcription factor binding based on the provided posterior probabilities.
• Analyzing predicted binding patterns for specific transcription factors like FOXA1 and CTCF mentioned in the description.
• Validating in silico ChIP-seq predictions against experimental datasets from the Cistrome and ENCODE-DREAM challenges.

Strengths

• Data is organized into two distinct archives for the Cistrome and ENCODE-DREAM validation datasets.
• Version 2.0.0 updates address missing predictions for FOXA1 and CTCF on specific chromosomes.
• Predictions are provided for specific, named chromosomes and cell types, offering concrete validation targets.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment.
• Last update date is unknown; freshness unverified.

Provenance

Source

University of Toronto, Mehran Karimzadeh

Collection Method

Computational predictions (Virtual ChIP-seq) generated for validation datasets.